The centromere is a specialized chromosomal locus that ensures proper segregation of chromosomes during mitotic and meiotic cell divisions. Centromeres are typically composed of large arrays of unrelated tandemly repeated DNAs encompassing several megabase regions that are poorly conserved between species (Lee et al., Hum. Genet., 100:291-304, 1997; Guenatri et al., J. Cell Biol., 166:493-505, 2004; Jiang et al., Trends Plant. Sci., 8:570-575, 2003).
In mouse, two types of repetitive DNA sequences are associated with centromeres. These are the major satellite repeats (approximately 6 megabase arrays of 234 bp per repeat unit) and minor satellite repeats (approximately 600 kb arrays of 120 bp per repeat unit) (Choo, The Centromere, Oxford University Press, Oxford, N.Y., Tokyo. 1997) that are distinct from human centromeric repeats. It has been shown that major satellite sequences are located in the pericentromeric region, forming clusters associated with heterochromatin protein 1 alpha, whereas minor satellite sequences coincide with the centric constriction of the centromere and is associated with centromere-specific proteins that are conserved from yeast to mammals (Vissel and Choo, Genomics, 5:407-414, 1989; Choo, The Centromere, Oxford University Press, Oxford, N.Y., Tokyo. 1997).
The centromeres of human chromosomes are characterized by several megabases (Mb) of alpha-satellite DNA (also known as alphoid DNA), which is composed of a tandem array of a 171 bp repeat unit. Alpha-satellite DNA is the only human centromeric DNA capable of de novo kinetochore formation. A number of groups have shown that alpha-satellite DNA cloned from human chromosomes or generated in vitro supports formation of Human Artificial Chromosomes (HACs) when introduced into cultured cells (Harrington et al., Nat. Genet., 15:345-355, 1997; Ikeno et al., Nat. Biotechnol., 16:431-439, 1998; Willard, Science, 290:1308-1309, 2000; Grimes et al., Mol. Ther. 5:798-805, 2002; Ohzeki et al., J. Cell. Biol., 159:765-775, 2002; Kouprina et al., Nucleic Acids Res., 31: 922-934, 2003; Basu and Willard, Trends Mol. Med., 11:251-258, 2005; Ebersole et al., Nuc. Acids Res., 33:e130, 2005).
A number of non-alphoid DNA repeats have been also identified in the pericentromeric regions of human chromosomes that flank alpha-satellite DNA arrays. For example, the classical satellites I, II, and III were detected in centromeric regions of human chromosomes 3, 4, 9, 13, 14, 15, 21, and 22 (Gosden et al., Exp Cell Res., 92:148-158, 1975; Vissel et al., Cytogenet. Cell Genet., 61:81-86, 1992; Meyne et al., Chromosoma, 103:99-103, 1994). A subset of beta-satellite DNA has been detected in the centromeric region of human chromosome 9 (Waye and Willard, Proc Natl Acad Sci USA., 86:6250-6254, 1989). The centromeric regions of the human acrocentric chromosomes harbor a sn5 satellite DNA (Johnson et al., Hum Mol Genet., 1:741-747, 1992) and gamma-satellite DNA has also been identified in the pericentromeric regions of human chromosomes 8, X, and Y (Lin et al., Chromosoma, 102:333-339, 1993; Lee et al., Chromosoma, 104:103-112, 1995; Lee et al., Chromosoma, 109:381-389, 2000). Gamma-satellite DNA is a tandem array of 220 bp, GC-rich repeating DNA monomers, usually forming 10-200 kb clusters flanked by alpha satellite DNA.
Despite the diversity in size and sequence of centromeric and pericentromeric DNA, the overall architecture and composition of centromeric chromatin is similar in different species. One hallmark of all functional centromeres is the presence of the H3 variant, CENP-A (Sullivan and Karpen, Nat Struct Mol Biol 11:1076-1083, 2004; Schueler and Sullivan, Ann Rev Genomics Hum Genet 7:301-313, 2006; Lam et al, Proc Natl Acad Sci USA 103:4186-4191, 2006; Black et al, Mol Cell 25:309-322, 2007). CENP-A is associated with the centromere/kinetochore, the large protein/DNA complex which attaches to spindle microtubes during mitosis and which includes highly homogeneous alpha-satellite DNA in human and minor satellite DNA in mouse. CENP-A nucleosomes represent open chromatin domains in the centromere core. In contrast, flanking pericentromeric DNA consisting of both highly diverged alphoid DNA and non-alphoid DNAs is assembled into heterochromatin lacking CENP-A (Schueler et al, Science 294: 109-115 2001; Schueler and Sullivan, 2006; Black et al, 2007).